Investigation of Polycystic Ovary Syndrome (PCOS) Diagnosis Using Machine Learning Approaches

Liver cirrhosis is a major global health problem causing millions of deaths annually, and timely detection with aggressive treatment can significantly improve patients' quality of life. Modelling complex diseases from biomedical data is computationally challenging due to high dimensionality, strong feature correlations, noise, and limited labelled samples. Conventional Machine Learning (ML) pipelines often struggle with robustness, interpretability, and generalisation under such conditions. In this study, we propose an ML-driven multi-stage decision framework for complex disease modelling and therapeutic exploration. The framework integrates single-cell transcriptomic profiling, high-dimensional network-based feature stabilisation, multi-model learning, deep representation construction, and post-hoc decision support. Specifically, single-cell sequencing data were analysed to identify key cellular subpopulations, followed by high-dimensional weighted gene co-expression network analysis (hdWGCNA) to stabilise gene modules under sparsity and noise. To enhance non-linear feature interaction modelling, tabular molecular features were restructured into two-dimensional disease maps and analysed using a CNN. Finally, molecular docking was incorporated as a decision-support module to evaluate candidate therapeutic compounds. Using liver cirrhosis as a representative case, the framework identified a disease-associated endothelial subpopulation and extracted seven robust signature genes (HSPB1, GADD45A, CLDN5, ATP1B3, C1QBP, ENPP2, and PARL). The CNN-based representation learning module outperformed conventional pipelines in classification. The framework is disease-agnostic and readily extends to other omics-driven biomedical applications involving uncertainty, heterogeneity, and limited samples.

Diabetes mellitus affects over 537 million adults worldwide and remains a major challenge in preventive healthcare. Existing machine-learning studies primarily formulate diabetes prediction as a binary classification problem, while subtype-oriented analysis and glycaemic-cognitive associations remain comparatively underexplored. We present a reproducible three-stage machine learning framework for diabetes detection, subtype-oriented clustering, and metabolic-cognitive association analysis. In Stage 1, five supervised classifiers together with a stacking ensemble are benchmarked on the NCSU Diabetes Dataset using stratified five-fold cross-validation and evaluation metrics including ROC-AUC, balanced accuracy, recall, and F1-score. SVM-RBF and Logistic Regression achieve the highest ROC-AUC ($0.825 \pm 0.026$), while Random Forest achieves the highest accuracy ($0.762 \pm 0.030$). SHAP explainability identifies Glucose, BMI, and Age as the dominant predictive biomarkers. In Stage 2, silhouette-validated K-Means clustering ($k=2$, silhouette $\approx 0.116$) is applied to confirmed diabetic cases using Glucose, Insulin, and Age, recovering clinically plausible subtype-oriented partitions without requiring ground-truth subtype labels. In Stage 3, statistical analysis of the Ohio Longitudinal Cognitive Dataset ($n=373$) reveals a significant positive association between glycaemic control and cognitive function ($ρ_s = 0.208$, $p = 5.29 \times 10^{-5}$), which survives Holm correction. The findings support the utility of statistically grounded and interpretable ML pipelines for reproducible diabetes analytics and subtype-aware exploratory analysis.

Discrepancies between clinical diagnoses and omics profiles within a characterized cohort may reflect misdiagnosis, hidden subgroups or prodromal disease states. We propose MLASDO, a tool to detect and characterize such discrepancies before downstream analyses. MLASDO (1) detects outliers using two unsupervised methods, thereby flagging potential poor-quality samples; and (2) identifies and characterizes anomalous samples (ASs), i.e., individuals whose molecular profile resembles the opposite clinical class. We applied MLASDO to the Parkinson's Progression Markers Initiative (PPMI) and Parkinson's Disease Biomarkers Program (PDBP) Parkinson's disease (PD) cohorts. In PPMI, it detected 26 outliers and 12 ASs: 5 anomalous healthy controls (AHCs) and 7 anomalous PD cases (APDs). AHCs exhibited higher cerebrospinal fluid (CSF) A\b{eta}1-42 levels than controls (P < 0.0396), suggesting resistance to cognitive decline. AHC-specific genes were enriched for the MAPK pathway (P<0.0145), implicated in PD pathogenesis. One AHC later received a different neurological disorder, three months after enrollment. In PDBP, it identified 10 outliers and 8 ASs: 2 AHCs and 6 APDs. One AHC exhibited 24 clinical features consistent with a PD-like phenotype, including severe motor impairment. Results are compiled in an interactive report for inspection and querying, highlighting clinically meaningful individuals otherwise overlooked in conventional analyses.